* use std::span for substruct match callbacks
This removes a copy from every evaluation of potential matches
* some cleanup/modernization
* some modernization
* deprecate chiralAtomCompat
* small optimization
* remove naked pointers
* improve new_timings.py script
* changes suggested in review
* response to review
* response to review
* add serialization to the TautomerQuery
* add to python wrapper
* changes in response to review
* put TautomerQueryCanSerialize in Python wrappers
* include serialization build dependency
* Swap to using a data structure for default normalization parameters
* bring the default fragment data into the code too
* cleanup
* add reionizer parameters via data
change fragment parse failures to ValueErrorExceptions
* tautomer parameters in the code
* got a little over-enthusiastic in that last cleanup
* use boost::flyweight to cache normalization and charge data params
* a bit more cleanup
* support reading params from JSON
* fragments from JSON
single-call for fragment removal
* add a one-liner for the canonical tautomer
* quick refactor
* Fixes#4115
* complete the parents
* docs
* move the definitions to a namespace and make them const
* see if switching to c++14 fixes the CI compile problems with g++ 5.5
* somewhat uglier way of solving the initalizer list problem
* set all source code files to have native line endings
* normalized all source code line endings
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* Fixes#3797
* [WIP] Add tautomer queries to the substruct library
* Add TautomerQuery to CMake
* Add missing TautomerQuery functions, python wrapper and tests
* Add python wrappers for Substruct Library Tautomer Queries
* Explictly label non-const pattern function now that we have both
* Use boost::shared_ptr not std::shared_ptr
* Fix java builds
* One more try to fix java builds
* Fix Java Tests
* Run clang format
* Reenable tests
* Fix annoyingly stupid bug and annoying commit of debug code
* Fix documentation
* reenable ifdef threadsafe check
* Throw warning and perform tautomer search instead of bailing with incorrect fingerprints
* Simplfy api with templates
* Fix SubstructLibrary java issues
* minor API cleanup
* simplify the SWIG wrappers
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Fixes#3821 copy constructor by making the template molecule a shared pointer
* Pushed a commit by accident, reverting
* Copy constructor now does a deep copy
* Add operator= test and ensure deep copies of template
* Update Code/GraphMol/TautomerQuery/catch_tests.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Remove extraneous .get()'s
* Add better testing names for catch test
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* - Added a TautomerEnumerator constructor which allows passing CleanupParameters
- Added three configurable parameters to CleanupParameters
- Added a callback to TautomerEnumerator
- Fixed a bug where the same tautomer could be mapped by both isomeric and non-isomeric SMILES
- TautomerEnumerator::enumerate() now returns a TautomerEnumeratorResult and does not take
dynamic_bitset pointers as optional parameters
- Added a missing transform from the Sitzmann paper
- General code cleanup and optimization
* - TautomerEnumeratorResult is now iterable in both C++ and Python
- further optimizations
- implemented a TautomerEnumerator.PickCanonical() Python wrapper
- added C++ and Python accessors to SMILES and SmilesTautomerMap
* - make sure the number of tautomers reported by rdLogger is correct and definitive
* make sure that if N maxTautomers are requested, N tautomers are returned if the theoretical number of tautomers is M>N
* avoid that sulfonic acids hit the formamidinesulfinic acid tautomerisation rule
* offer an option to allow the old API to still be used.
* Changes in response to review and following discussion with Gareth and Greg
* - made TautomerEnumeratorResult an enum class (was a plain C enum)
- made TautomerEnumeratorResult::const_iterator a bidirectional_iterator
- added tests to fully probe the TautomerEnumeratorResult::const_iterator functionality
* - change the difference_type definition
- added tests for the above
* - cosmetic change to improve code readability
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* TautomerQuery class
* working test
* Comment header
* Merge with master. Greg's suggestions. More tests. Python wrapper
* Updated Pattern Fingerprints to merge with master. Reset email
* Java/C# wrappers. Java test
* Java/C# wrappers. Java test
* Java/C# wrappers. Java test
* Greg suggestions of 6_2_2020
* Explicit types in Java TautomerQueryTests class
* Update Code/GraphMol/QueryOps.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* get windows dll builds working
* Removed tautomer query wrappers from RDKit namespace
* Fixes from evaluation
* Template molecule identification fix. Greg's suggestion
* Final check search functor for evaluating template matches as they are found
Co-authored-by: Gareth Jones <gjones@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
